vdsstream VDS - Target - Glyceraldehyde-3-phosphate dehydrogenase (T. Brucei)

Organism: Trypanosoma Brucei
Target: Glyceraldehyde-3-phosphate Dehydrogenase
NCBI GENE # or RefSeq#: 3658068
EC #: 1.2.1.12
Length of Protein: 359 residues
Total Size of Gene: 1080 nt
Molecular Weight: 39048 Da
Druggability: 0.8
DNAWorks Output File
Essentiality: Glycolysis as a target for the design of new anti-trypanosome drugs

1.2.1.12 Reaction Diagram.png

Assay: https://docs.google.com/open?id=0B4O2KqKh2q_-RmNhM1U1VXpLY2M
Cost of Assay: https://docs.google.com/open?id=0B4O2KqKh2q_-SU53NTR5UFJMYWs

What	Cost	What you get	Concentration	Product #
Triethanolamine hydrochloride	29.8	100g		T1502
D-(−)-3-Phosphoglyceric acid disodium salt	13	only 10mg, the next step up is 1g for 230ish		P8752
L-Cysteine Hydrochloride	8.7	.5g (might needs more)		C7880
Sodium Bicarbonate	33	500g		S8875
β-Nicotinamide adenine dinucleotide, reduced disodium salt hydrate	22.6	50mg		N8129
Adenosine 5′-triphosphate disodium salt hydrate	64	1g		A7699
3-Phosphoglyceric Phosphokinase	53	2KU		P7634
Glyceraldehyde-3-Phosphate Dehydrogenase Enzyme Solution	38	500 units		G2267

GAPDH pdb ID 2X0N

Use these to find active site: 3CIF, 3CMC, 1NQA
Forward:
TACTTCCAATCCATGACCATCAAAGTTGGCATT
Reverse:

TATCCACCTTTACTGTTACAGCTTTGCAGCACGGTC
Primer Melting Temperatures:

Upstream		mM Mg++
		0	1.5	2	4	6
bp	20	61.6	69.4	70	71	71.5
	19	61.5	69.3	69.8	70.8	71.3
	18	61.9	69.6	70.1	71.2	71.7

Downstream		mM Mg++
		0	1.5	2	4	6
bp	20	67.2	74.2	74.7	75.4	75.8
	19	66.1	73.2	73.6	74.5	74.9
	18	65.2	72.3	72.8	73.7	74.1

Active Site Coordinates:
X: 70.858
Y: 20.161
Z: 48.768
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=49791969&loc=ec_rcs
Original substrate

http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=9875131
Found from bindingdb with a Ki of 2000nM

http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=945&loc=ec_rcs
found from http://www.sciencedirect.com/science/article/pii/S0003986105003048
Article says IC50 of 0.25uM

http://pubs.acs.org/doi/abs/10.1021/bi00167a028
Gives
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=282522&loc=ec_rcs
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=124361&loc=ec_rcs
and "compound 6"

http://ajpheart.physiology.org/content/299/4/H1212
gives
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=3359494

Compound	CID	MW	logP	Rotatable Bonds	Polar Surface Area	H Donors	H Acceptors
3-phosphoglycerate	49791969	182	-2.1	2	133	1	7
SureCN4142096	9875131	342	7.6	13	57.5	2	3
nitroxyl	945	31	0.2	0	40.9	1	2
arenaemycin E	282522	276	0.6	1	76.1	1	5
heptelidic acid	124361	280	1.4	2	76.1	1	5
S-nitrosocysteine	3359494	150	-3.4	3	118	2	6

Average		210.1667	0.716667	3.5	83.6	1.333333	4.66666667